DNA Algorithm implementations you may currently download

The Octave/Matlab versions of FireSat runs on Windows and Linux. Please contact me if you require the mex's for your specifc configuration.
FireSat implements functionality to find TRs of lengths 10 to 1000. Three versions
are provided. However only the final version has been more fully analised and optimized for
accuracy using an ROC analysis.

The main is "/phd_cdr_implement/firesat_3/15_fsat/latest/try_do_find_trs_110_default.m".

Parameters are currently set to default but can be tweaked by editing them in the preampble of this file using either Matlab or Octave. The current run time for this example in Octave is 26s and on Matlab 2.6s on a Dell Precision laptop with an 6th generation i7 processor.

The advanced commandline version runs on Windows and Linux.
It has added functionality including that it finds TRs of length 1 to 6.
One can add TranscriptInfo as parameter and can only partially parse an input
file if one so wishes. A batch file is included in th zip as an example of usage.

The relative substring error version runs on Windows and was
implemented by calculating thresholds based on the relative
substring error. The relative substring error is defined as the
substring error here and
here.

The FireµSat2 Input/Output document provides a description
of the usage and range for the input parameters of FireµSat2.
A discussion of the output format of FireµSat2 is also
included (applicable to all versions).

Results of the verification of a published comparative study on PTR detection